From 594bd3ec774f0027248f2d7ef2e299c5c868fae6 Mon Sep 17 00:00:00 2001
From: KristinaGomoryova <gomoryova@sci.muni.cz>
Date: Fri, 18 Oct 2024 11:46:46 +0200
Subject: [PATCH] odd electron ions assignment based on ionMode

---
 tools/mfassignr/macros.xml                |  8 ++++----
 tools/mfassignr/mfassignr_mfassignCHO.xml | 17 +++++++++++++++--
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/tools/mfassignr/macros.xml b/tools/mfassignr/macros.xml
index df45ec4b..2d8aa58e 100644
--- a/tools/mfassignr/macros.xml
+++ b/tools/mfassignr/macros.xml
@@ -95,10 +95,10 @@
         <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000"
                help= "Upper limit of molecular mass to be assigned."/>
         <section name="advanced" title="Advanced" expanded="false">
-              <param name="POEx" type="float" label="POEx" value="0"
-               help= "If set to 1 and ionMode is positive, positive mode odd electron ions can be assigned."/>              
-              <param name="NOEx" type="float" label="NOEx" value="0"
-               help= "If set to 1 and ionMode is negative, negative mode odd electron ions can be assigned."/> 
+              <param name="assign_typeof_ions" type="select" display="radio" label="Assign odd electron ions based on the ionization mode?" help="This parameter determines whether to assign either positive mode odd electron ions (if ionMode is positive) or negative mode odd electron ions (if ionMode is negative).">
+                     <option value="yes">yes</option>
+                     <option value="no" selected="true">no</option>
+              </param>
               <param name="Ex" type="integer" label="Amount of Chlorine 37" value="0" help= "Sets the amount of Chlorine 37 to be used in assignment."/>  
               <param name="Mx" type="integer" label="Amount of Sodium adduct" value="0" help= "Sets the amount of Sodium adduct to be used in assignment."/>       
               <param name="NH4x" type="integer" label="Amount of Ammonium adduct" value="0" help= "Sets the amount of Ammonium adduct to be used in assignment."/>     
diff --git a/tools/mfassignr/mfassignr_mfassignCHO.xml b/tools/mfassignr/mfassignr_mfassignCHO.xml
index a3e00949..27d4dd56 100644
--- a/tools/mfassignr/mfassignr_mfassignCHO.xml
+++ b/tools/mfassignr/mfassignr_mfassignCHO.xml
@@ -22,6 +22,19 @@
         iso <- read.delim("$input_iso", sep="\t")
         #end if
         SN = $sn_ratio * $kmdn
+        POEx = 0
+        NOEx = 0
+        
+        #if "$assign_typeof_ions"=="yes"
+            #if $ionMode=="pos"
+            POEx = 1
+            NOEx = 0
+            #end if
+            #if $ionMode=="neg"
+            POEx = 0
+            NOEx = 1
+            #end if
+        #end if        
 
         MF_CHO_assign <- MFAssignR::MFAssignCHO(
             peaks = mono,
@@ -33,8 +46,8 @@
             highMW = $highMW,
             ppm_err = $ppm_err,
             SN = SN,
-            POEx = $POEx, 
-            NOEx = $NOEx,
+            POEx = POEx, 
+            NOEx = NOEx,
             Ex = $Ex,
             Mx = $Mx,
             NH4x = $NH4x,